Transcriptomic analysis of NDRG1 amplification in aggressive breast cancer

Background: Inflammatory breast cancer (IBC) is a rare but highly aggressive variant of breast cancer, accounting for 10% of breast cancer-related deaths. We have identified NDRG1, located on chromosome 8q24.3 near MYC within a commonly amplified region, as a key promoter of tumor growth and progression in IBC models and is associated with poor survival outcomes. Unlike many oncogenes, NDRG1 is rarely deleted or silenced and is more frequently expressed in IBC compared to non-IBC tumors. A recent study reported NDRG1 amplification in 42% of triple-negative IBC cases. We hypothesize that NDRG1 amplification in triple-negative IBC is associated with distinct gene expression profiles and enrichment of oncogenic pathways that contribute to the aggressive phenotype of the disease. Methods: RNA sequencing data from 19 triple-negative IBC tumors (8 NDRG1 amplified, 11 non-amplified) were analyzed using DEseq2 package. Heatmaps were generated to visualize clustering and expression differences. Gene Set Enrichment Analysis (GSEA) was performed using Hallmark and KEGG pathway databases. Publicly available TCGA and METABRIC breast cancer datasets were used to assess NDRG1 amplification and its association with mRNA/protein expression and survival outcomes. Results . Among the 19 triple-negative tumors analyzed, 8 (42%) exhibited NDRG1 amplification, which was significantly correlated with increased RNA expression (p = 0.05). Differential expression analysis identified CALCA , RHO , DPYSL5 , GPR101 , ZIC3 , and IRS4 as the most upregulated, and SERPINA6 , SCGB3A1 , PI3 , LRG1 , DAPL1 , MYEOV as the most downregulated in NDRG1 -amplified tumors. GSEA revealed enrichment of DNA repair, cell cycle, mTOR signaling, and MYC target pathways, and downregulated pathways included interferon gamma response, estrogen response and NFkB pathway. TCGA and METABRIC analyses confirmed that NDRG1 amplification correlates with elevated mRNA expression (p<0.0001) and elevate protein levels (p<0.0001) and poorer overall survival (p=0.013, TCGA; p=0.0002, METABRIC). Conclusions: NDRG1 amplification marks a transcriptionally distinct subset of triple-negative IBC, enriched in proliferative and DNA repair pathways. These molecular features highlight its potential as a biomarker of aggressive disease biology and potential target for further mechanistic investigation and therapeutic intervention.